BN1750 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.1755e-06 1.0385e-02
Layer 4 1.4222e-05 1.7619e-03
Layer 6 1.3541e-04 1.6227e-03
Layer 5 1.4650e-04 6.4458e-04
WM 4.1146e-03 7.5853e-02
Layer 1 7.2530e-02 2.6401e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.8936 0.6964
SNCB Layer 5 2.8369 0.6861
PRKAR1B Layer 5 2.8740 0.6751
CELF4 Layer 4 3.1562 0.6664
RAB6B Layer 5 2.7363 0.6651
ENO2 Layer 5 2.7852 0.6640
ATP1B1 Layer 5 3.0000 0.6630
SNAP25 Layer 5 3.0391 0.6625
GDI1 Layer 5 2.4727 0.6622
APBB1 Layer 4 2.7881 0.6614
SYN1 Layer 5 2.6426 0.6583
TUBB2A Layer 5 2.8145 0.6565
EEF1A2 Layer 5 2.7129 0.6543
FXYD6 Layer 4 2.9697 0.6535
PI4KA Layer 5 2.5391 0.6506
DGKZ Layer 5 2.5215 0.6504
SYNGR1 Layer 4 3.1602 0.6492
BASP1 Layer 5 2.7422 0.6476
CHN1 Layer 4 2.9414 0.6470
STX1B Layer 4 3.0352 0.6469
RAB3A Layer 6 2.6484 0.6465
AP2M1 Layer 5 2.6602 0.6454
PREPL Layer 5 2.7793 0.6446
SH3GL2 Layer 4 2.9863 0.6433
CALY Layer 5 3.0029 0.6412
MTCH1 Layer 5 2.8398 0.6400
DYNLL2 Layer 5 2.6045 0.6395
ARHGDIA Layer 5 2.5537 0.6375
YWHAG Layer 5 2.8711 0.6367
SPOCK1 Layer 5 2.6426 0.6359
CALM3 Layer 4 2.6309 0.6358
TAGLN3 Layer 5 2.6895 0.6358
PFKP Layer 5 2.6396 0.6347
B4GAT1 Layer 5 2.8516 0.6337
HLF Layer 4 2.6260 0.6334
UCHL1 Layer 5 2.8281 0.6331
APP Layer 5 2.9219 0.6313
CXXC5 Layer 5 2.3027 0.6294
SSBP3 Layer 4 2.6836 0.6285
NSF Layer 5 2.9277 0.6282
CHGA Layer 4 3.6016 0.6257
USP22 Layer 3 2.4941 0.6254
SYT4 Layer 5 2.7793 0.6229
STMN1 Layer 4 3.0518 0.6214
YPEL3 Layer 5 2.7275 0.6211
SIRPA Layer 5 2.5586 0.6200
ADAR Layer 4 2.5146 0.6200
GPI Layer 4 2.8340 0.6192
NELL2 Layer 5 2.4482 0.6191
NEUROD2 Layer 4 2.9414 0.6185

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1750
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1750_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1750/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1750/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1750/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1750/report/PD/BN1750_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1750/report/PD/BN1750_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 06:50:30
  • Number of Processes: 10
  • Spending Time: 0h 1m